Kocarek - Pharmacogenetics

Question 1

Pharmacogenetics/Pharmacogenomics definition:

Answer 1

study of genetically controlled variations in drug response, and includes both genetic polymorphisms and rare genetic defects that alter an individual’s drug response

Question 2

Genetic Polymorphisms

Answer 2

a Mendelian or monogenic trait that exists in the population in at least two phenotypes, neither of which is rare (>1-2%)

Question 3

What is used to treat acute lymphoblastic leukemia and what gene variation prevents metabolism and can be fatal?

Answer 3

6-mercaptopurine (6-MP) is used to treat childhood ALL.

1 in 300 children has a variant gene for thiopurine methyltransferase that prevents 6-MP metabolism; drug accumulates in those children and can be fatal

Question 4

What is clopidogrel and what does it require for conversion to its active form?

Answer 4

clopidogrel (plavix) is an anti-platelet drug that is used in addition to aspirin to prevent CV events in high risk pts.

Requires metabolism by CYP2C19 for conversion to active form

Without CYP2C19, clopidogrel builds up, therefore you need to know if the pt is a CYP2C19 poor metabolizer

Question 5

What is the cause of isoniazid-induced neuropathy in some individuals?

Answer 5

NAT2 deficiency

Question 6

What causes prolonged apnea after succinylcholine?

Answer 6

pseudocholinesterase deficiency

Question 7

What breaks down debrisoquine (anti-hypertensive used in 1975 by Dr. Robert Smith)? What is the product?

Answer 7

Debrisoquine is converted to 4-hydroxydebrisoquine (inactive metabolite) by CYP2D6

Question 8

Ultrarapid metabolizer for debrisoquine

Answer 8

multiple copies of CYP2D6

Question 9

How can one estimate the fraction of phenotypic variability that is attributable to genetic factors?

Answer 9

Twin studies - monozygotic vs. dizygotic

Multigenerational kindred studies - interfamily vs. intrafamily variability

Question 10

Additive (Codominant) Traits

Answer 10

Most common pattern

No domination of one allele over the other

Gene dosage effect
o AA= 2 good alleles, 100% function
o Aa= 1 good allele and 1 mutant allele, 50% function
o Aa= 2 mutant alleles, little/no function

Ex: CYP2C19 poor metabolizer

Question 11

Autosomal Recessive

Answer 11

Normal allele dominates over mutant allele
o AA= 100% function
o Aa= 100% function
o aa= little/no function

Ex: CYP2D6 poor metabolizer

Question 12

Autosomal Dominant

Answer 12

Only those with both good alleles have normal activity
o AA=100% function
o Aa and aa= little/ no function

Question 13

What is the recommended starting dose for warfarin determined by?

Answer 13

CYP2C9 - metabolizes and inactivates warfarin

VKORC1 - pharmacological target of warfarin

Question 14

Major types of polymorphism (3)

Answer 14

Single nucleotide polymorphisms (SNPs)
Insertions/deletions (Indels)
Copy number variations (CNV)

Question 15

Single nucleotide polymorphisms (SNPs)

Answer 15

One every few hundred

About 10 million SNPs

Question 16

Copy number variations (CNV)

Answer 16

~10% of the genome
Segment of DNA in which a variable number of that segment has been found in one or more populations
Duplications, deletions, inversions
CYP2D6 duplications associated with ultrarapid metabolizer phenotype

Question 17

cSNPs

Types:

Answer 17

SNPs in coding region

Non-synonymous (missense) - aa change
Synonymous (sense) - no aa change
Nonsense - stop codon

Question 18

Polymorphisms in non-coding regions (4)

Answer 18

5’ and 3’ untranslated regions of mRNA

Promoter and enhancer regions of genes

Introns

Intergenic regions

Question 19

Polymorphisms in 5’ and 3’ untranslated regions of mRNA

Answer 19

may alter cis-elements that determine mRNA translatability or stability

Question 20

Polymorphisms in Promoter and enhancer regions of genes

Answer 20

may alter cis-elements that regulate gene transcription

Question 21

Polymorphisms in introns

Answer 21

When near exon-intron boundaries, may affect transcript splicing - would often introduce a frame shift and a premature stop codon

Question 22

Polymorphisms in intergenic regions

Answer 22

may affect DNA tertiary structure, interaction with chromatin and topoisomerases, or DNA replication

Question 23

Where are most of the SNPs?

Answer 23

most of the SNPs are within introns or intergenic regions.

Question 24

What does CYP3A5*3 indicate?

Answer 24

The CYP3A5*3 allele contains a SNP in intron 3 that creates an alternative splice site, which results in introduction of an early stop codon and production of an inactive protein.

Question 25

Haplotype

Answer 25

Haplotype - a set of SNPs on a single chromosome that is statistically associated The particular combination of all variants that occurs together for a gene (wiki) A combination of alleles (DNA sequences) at adjacent locations (loci) on a chromosome that are inherited together. A gene is likely to have more than one SNP – the haplotype is the particular combination of all SNPs

Question 26

ABCB1 gene has SNPs at base pair 3421 (T or A) and 3435 (C or T), what are the possible haplotypes?

Answer 26

``` The possible haplotypes would be: • T3421C3435 • T3421T3435 • A3421C3435 • A3421T3435 ```

Question 27

Linkage definition: 2 types:

Answer 27

Definition: The extent to which the genotypes at two genetic loci are independent of one another. Linkage equilibrium – the genotype present at one locus is independent of the genotype at a second locus Linkage disequilibrium – the genotypes at the two loci are not independent of one another Note:In complete linkage disequilibrium, genotypes at two loci always occur together

Question 28

Penetrance

Answer 28

Penetrance: proportion of individuals carrying a variant allele that express an associated phenotype

Question 29

Clinical relevance of a polymorphism is determined by (4):

Answer 29

Frequency and penetrance of a variant allele Narrowness of therapeutic index or sharpness of dose-response curve Limited availability of alternative clearance pathways Absence of alternative drugs

Question 30

What type of varient has the highest predicted risk to the phenotype?

Answer 30

Nonsense

Question 31

What types of genes are involved in pharmacogenetic traits?

Answer 31

Genes that encode determinants of a drug’s pharmacokinetics o e.g., Drug-metabolizing enzymes, transporters Genes that encode drug receptors and targets o Variants with profound functional consequences may cause disease phenotypes that cause negative selective pressure o However, variants that cause more subtle changes can be maintained in a population without causing disease but may cause variation in drug response Genes that are involved in the disease being treated but do not directly interact with a drug (modifiers) (determinants, receptor/target, disease but don't interact with drug)

Question 32

Why is UGT1A1 important? What happens with a UGT1A1 defect? What are some genetic diseases attributable to UGT1A1?

Answer 32

it metabolizes bilirubin hyperbilirubinemia Specific genetic diseases that are attributable to UGT1A1 polymorphisms include Crigler-Najjar syndrome types I and II and Gilbert’s syndrome.

Question 33

What 2 enzymes catalyze N-acetylation? | Which one is the primary polymorphic one?

Answer 33

Two major enzymes catalyze N-acetylation– N-acetyltransferases 1 and 2 (NAT1 and NAT2) NAT2 is primary one that is polymorphic NAT1 was thought not to be polymorphic, but recent evidence suggests that it also exhibits genetic polymorphisms

Question 34

N-acetyltransferases 2 (NAT 2) catalyzes: (3 examples)

Answer 34

NAT2 catalyzes the N-acetylation of a large number of drugs and environmental chemicals: e.g., procainamide, caffeine, 4-aminobiphenyl (human bladder carcinogen) • NAT2 shows considerable ethnic variation: Slow acetylators account for 90% in other groups

Question 35

Acetylation polymorphism: slow acetylators Slow acetylation is associated with several clinically important consequences (3): isoniazid tx: sulfa drug tx: arylamin carcinaogens:

Answer 35

Slow acetylators more prone to polyneuropathy during isoniazid treatment Slow acetylators more likely to develop hemolytic anemia during treatment with sulfa drugs Incidence of bladder cancer greater in slow acetylators exposed to arylamine carcinogens

Question 36

What is a consequence of fast acetylators?

Answer 36

“Fast” acetylators require larger doses to achieve a given desired effect

Question 37

Human acetylation polymorphism controlled by 4 major alleles at a single autosomal gene locus on: Slow vs. Fast acetylation: Dominance:

Answer 37

Human acetylation polymorphism controlled by 4 major alleles at a single autosomal gene locus on chromosome 8 o 3 alleles encode for slow activity; 1 allele encodes for fast activity o Fast activity is dominant – an individual must have 2 slow alleles to be a slow acetylator

Question 38

How many ADH enzymes in humans? Classes? Which class is the major ethanol-metabolizing enzyme?

Answer 38

Humans have 7 ADH enzymes grouped into 5 classes (I-V) | o Class I enzymes are major ethanol-metabolizing enzymes

Question 39

Nomenclature: ADH1 = ADH2 = ADH3 =

Answer 39

Nomenclature: ADH1 = ADH1A, encodes α polypeptide ADH2 = ADH1B, encodes β polypeptide ADH3 = ADH1C, encodes γ polypeptide

Question 40

Comparison of ADHs in Caucasians, East Asians, and individuals of African descent

Answer 40

Majority of Caucasians (about 95%) have ADH2*1 allele; about 50% ADH3*1 and ADH3*2 Majority of Japanese, Chinese, and Koreans have ADH2*2 allele ADH2*3 observed in ~15% of individuals of African descent; rest have ADH2*1; ADH3*1 in ~95%

Question 41

Comparison between ADH2*2 and ADH2*1. | What other polymorphism may occur with ADH2*2?

Answer 41

Individuals with the ADH2*2 genotype metabolize ethanol more rapidly than do those with the ADH2*1. Faster ethanol metabolism results in increased production of acetaldehyde, which is the toxic metabolite that causes alcohol induced flushing. Some individuals also have a polymorphism in the aldehyde dehydrogenase enzyme (ALDH2*2) that decreases its ability to convert the acetaldehyde into acetic acid. Since these individuals both produce more acetaldehyde and are less able to detoxify it, they are particularly prone to flushing.

Question 42

ADH Genotype/Isoenzyme

Answer 42

ADH2*1 - beta1beta2 ADH2*2 - beta2beta2 ADH2*3 - beta3beta3

Question 43

EtOH to Acetyl-CoA formula

Answer 43

EtOH --ADH--> Acetaldehyde (Toxic) --ALDH-->Acetic acid ----> Acetyl-CoA

Question 44

What ADH genotype has the highest/lowest Vmax?

Answer 44

``` Highest = 400 min-1: ADH2*2 Lowest = 9 min-1: ADH2*1 ```